X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/6eb3d1fb8fe71623fa63da46c250184cf2e4fbb8..78af1220d9e2ddf4d933d9a9487397414d8a3909:/sdk/python/arvados/collection.py diff --git a/sdk/python/arvados/collection.py b/sdk/python/arvados/collection.py index 30828732d8..38e794c24a 100644 --- a/sdk/python/arvados/collection.py +++ b/sdk/python/arvados/collection.py @@ -487,7 +487,8 @@ class RichCollectionBase(CollectionBase): def __init__(self, parent=None): self.parent = parent - self._modified = True + self._committed = False + self._callback = None self._items = {} def _my_api(self): @@ -537,24 +538,24 @@ class RichCollectionBase(CollectionBase): if item is None: # create new file if create_type == COLLECTION: - item = Subcollection(self) + item = Subcollection(self, pathcomponents[0]) else: - item = ArvadosFile(self) + item = ArvadosFile(self, pathcomponents[0]) self._items[pathcomponents[0]] = item - self._modified = True + self._committed = False self.notify(ADD, self, pathcomponents[0], item) return item else: if item is None: # create new collection - item = Subcollection(self) + item = Subcollection(self, pathcomponents[0]) self._items[pathcomponents[0]] = item - self._modified = True + self._committed = False self.notify(ADD, self, pathcomponents[0], item) if isinstance(item, RichCollectionBase): return item.find_or_create(pathcomponents[1], create_type) else: - raise IOError((errno.ENOTDIR, "Interior path components must be subcollection")) + raise IOError(errno.ENOTDIR, "Not a directory: '%s'" % pathcomponents[0]) else: return self @@ -567,7 +568,7 @@ class RichCollectionBase(CollectionBase): """ if not path: - raise errors.ArgumentError("Parameter 'path' must not be empty.") + raise errors.ArgumentError("Parameter 'path' is empty.") pathcomponents = path.split("/", 1) item = self._items.get(pathcomponents[0]) @@ -580,15 +581,20 @@ class RichCollectionBase(CollectionBase): else: return item else: - raise IOError((errno.ENOTDIR, "Interior path components must be subcollection")) + raise IOError(errno.ENOTDIR, "Is not a directory: %s" % pathcomponents[0]) - def mkdirs(path): + @synchronized + def mkdirs(self, path): """Recursive subcollection create. - Like `os.mkdirs()`. Will create intermediate subcollections needed to - contain the leaf subcollection path. + Like `os.makedirs()`. Will create intermediate subcollections needed + to contain the leaf subcollection path. """ + + if self.find(path) != None: + raise IOError(errno.EEXIST, "Directory or file exists: '%s'" % path) + return self.find_or_create(path, COLLECTION) def open(self, path, mode="r"): @@ -615,7 +621,7 @@ class RichCollectionBase(CollectionBase): create = (mode != "r") if create and not self.writable(): - raise IOError((errno.EROFS, "Collection is read only")) + raise IOError(errno.EROFS, "Collection is read only") if create: arvfile = self.find_or_create(path, FILE) @@ -623,9 +629,9 @@ class RichCollectionBase(CollectionBase): arvfile = self.find(path) if arvfile is None: - raise IOError((errno.ENOENT, "File not found")) + raise IOError(errno.ENOENT, "File not found") if not isinstance(arvfile, ArvadosFile): - raise IOError((errno.EISDIR, "Path must refer to a file.")) + raise IOError(errno.EISDIR, "Is a directory: %s" % path) if mode[0] == "w": arvfile.truncate(0) @@ -633,26 +639,31 @@ class RichCollectionBase(CollectionBase): name = os.path.basename(path) if mode == "r": - return ArvadosFileReader(arvfile, name, mode, num_retries=self.num_retries) + return ArvadosFileReader(arvfile, num_retries=self.num_retries) else: - return ArvadosFileWriter(arvfile, name, mode, num_retries=self.num_retries) + return ArvadosFileWriter(arvfile, mode, num_retries=self.num_retries) - @synchronized def modified(self): - """Test if the collection (or any subcollection or file) has been modified.""" - if self._modified: - return True - for k,v in self._items.items(): - if v.modified(): - return True - return False + """Determine if the collection has been modified since last commited.""" + return not self.committed() + + @synchronized + def committed(self): + """Determine if the collection has been committed to the API server.""" + + if self._committed is False: + return False + for v in self._items.values(): + if v.committed() is False: + return False + return True @synchronized - def set_unmodified(self): - """Recursively clear modified flag.""" - self._modified = False + def set_committed(self): + """Recursively set committed flag to True.""" + self._committed = True for k,v in self._items.items(): - v.set_unmodified() + v.set_committed() @synchronized def __iter__(self): @@ -683,7 +694,7 @@ class RichCollectionBase(CollectionBase): def __delitem__(self, p): """Delete an item by name which is directly contained by this collection.""" del self._items[p] - self._modified = True + self._committed = False self.notify(DEL, self, p, None) @synchronized @@ -715,33 +726,33 @@ class RichCollectionBase(CollectionBase): """ if not path: - raise errors.ArgumentError("Parameter 'path' must not be empty.") + raise errors.ArgumentError("Parameter 'path' is empty.") pathcomponents = path.split("/", 1) item = self._items.get(pathcomponents[0]) if item is None: - raise IOError((errno.ENOENT, "File not found")) + raise IOError(errno.ENOENT, "File not found") if len(pathcomponents) == 1: if isinstance(self._items[pathcomponents[0]], RichCollectionBase) and len(self._items[pathcomponents[0]]) > 0 and not recursive: - raise IOError((errno.ENOTEMPTY, "Subcollection not empty")) + raise IOError(errno.ENOTEMPTY, "Subcollection not empty") deleteditem = self._items[pathcomponents[0]] del self._items[pathcomponents[0]] - self._modified = True + self._committed = False self.notify(DEL, self, pathcomponents[0], deleteditem) else: item.remove(pathcomponents[1]) def _clonefrom(self, source): for k,v in source.items(): - self._items[k] = v.clone(self) + self._items[k] = v.clone(self, k) def clone(self): raise NotImplementedError() @must_be_writable @synchronized - def add(self, source_obj, target_name, overwrite=False): - """Copy a file or subcollection to this collection. + def add(self, source_obj, target_name, overwrite=False, reparent=False): + """Copy or move a file or subcollection to this collection. :source_obj: An ArvadosFile, or Subcollection object @@ -753,24 +764,74 @@ class RichCollectionBase(CollectionBase): :overwrite: Whether to overwrite target file if it already exists. + :reparent: + If True, source_obj will be moved from its parent collection to this collection. + If False, source_obj will be copied and the parent collection will be + unmodified. + """ if target_name in self and not overwrite: - raise IOError((errno.EEXIST, "File already exists")) + raise IOError(errno.EEXIST, "File already exists") modified_from = None if target_name in self: modified_from = self[target_name] - # Actually make the copy. - dup = source_obj.clone(self) - self._items[target_name] = dup - self._modified = True + # Actually make the move or copy. + if reparent: + source_obj._reparent(self, target_name) + item = source_obj + else: + item = source_obj.clone(self, target_name) + + self._items[target_name] = item + self._committed = False if modified_from: - self.notify(MOD, self, target_name, (modified_from, dup)) + self.notify(MOD, self, target_name, (modified_from, item)) + else: + self.notify(ADD, self, target_name, item) + + def _get_src_target(self, source, target_path, source_collection, create_dest): + if source_collection is None: + source_collection = self + + # Find the object + if isinstance(source, basestring): + source_obj = source_collection.find(source) + if source_obj is None: + raise IOError(errno.ENOENT, "File not found") + sourcecomponents = source.split("/") else: - self.notify(ADD, self, target_name, dup) + source_obj = source + sourcecomponents = None + + # Find parent collection the target path + targetcomponents = target_path.split("/") + + # Determine the name to use. + target_name = targetcomponents[-1] if targetcomponents[-1] else sourcecomponents[-1] + + if not target_name: + raise errors.ArgumentError("Target path is empty and source is an object. Cannot determine destination filename to use.") + + if create_dest: + target_dir = self.find_or_create("/".join(targetcomponents[0:-1]), COLLECTION) + else: + if len(targetcomponents) > 1: + target_dir = self.find("/".join(targetcomponents[0:-1])) + else: + target_dir = self + + if target_dir is None: + raise IOError(errno.ENOENT, "Target directory not found.") + + if target_name in target_dir and isinstance(self[target_name], RichCollectionBase) and sourcecomponents: + target_dir = target_dir[target_name] + target_name = sourcecomponents[-1] + + return (source_obj, target_dir, target_name) @must_be_writable @synchronized @@ -792,35 +853,35 @@ class RichCollectionBase(CollectionBase): :overwrite: Whether to overwrite target file if it already exists. """ - if source_collection is None: - source_collection = self - # Find the object to copy - if isinstance(source, basestring): - source_obj = source_collection.find(source) - if source_obj is None: - raise IOError((errno.ENOENT, "File not found")) - sourcecomponents = source.split("/") - else: - source_obj = source - sourcecomponents = None + source_obj, target_dir, target_name = self._get_src_target(source, target_path, source_collection, True) + target_dir.add(source_obj, target_name, overwrite, False) - # Find parent collection the target path - targetcomponents = target_path.split("/") + @must_be_writable + @synchronized + def rename(self, source, target_path, source_collection=None, overwrite=False): + """Move a file or subcollection from `source_collection` to a new path in this collection. - # Determine the name to use. - target_name = targetcomponents[-1] if targetcomponents[-1] else (sourcecomponents[-1] if sourcecomponents else None) + :source: + A string with a path to source file or subcollection. - if not target_name: - raise errors.ArgumentError("Target path is empty and source is an object. Cannot determine destination filename to use.") + :target_path: + Destination file or path. If the target path already exists and is a + subcollection, the item will be placed inside the subcollection. If + the target path already exists and is a file, this will raise an error + unless you specify `overwrite=True`. - target_dir = self.find_or_create("/".join(targetcomponents[0:-1]), COLLECTION) + :source_collection: + Collection to copy `source_path` from (default `self`) - if target_name in target_dir and isinstance(self[target_name], RichCollectionBase) and sourcecomponents: - target_dir = target_dir[target_name] - target_name = sourcecomponents[-1] + :overwrite: + Whether to overwrite target file if it already exists. + """ - target_dir.add(source_obj, target_name, overwrite) + source_obj, target_dir, target_name = self._get_src_target(source, target_path, source_collection, False) + if not source_obj.writable(): + raise IOError(errno.EROFS, "Source collection is read only.") + target_dir.add(source_obj, target_name, overwrite, True) def portable_manifest_text(self, stream_name="."): """Get the manifest text for this collection, sub collections and files. @@ -834,6 +895,7 @@ class RichCollectionBase(CollectionBase): """ return self._get_manifest_text(stream_name, True, True) + @synchronized def manifest_text(self, stream_name=".", strip=False, normalize=False): """Get the manifest text for this collection, sub collections and files. @@ -877,7 +939,7 @@ class RichCollectionBase(CollectionBase): """ - if self.modified() or self._manifest_text is None or normalize: + if not self.committed() or self._manifest_text is None or normalize: stream = {} buf = [] sorted_keys = sorted(self.keys()) @@ -917,15 +979,15 @@ class RichCollectionBase(CollectionBase): holding_collection = Collection(api_client=self._my_api(), keep_client=self._my_keep()) for k in self: if k not in end_collection: - changes.append((DEL, os.path.join(prefix, k), self[k].clone(holding_collection))) + changes.append((DEL, os.path.join(prefix, k), self[k].clone(holding_collection, ""))) for k in end_collection: if k in self: if isinstance(end_collection[k], Subcollection) and isinstance(self[k], Subcollection): changes.extend(self[k].diff(end_collection[k], os.path.join(prefix, k), holding_collection)) elif end_collection[k] != self[k]: - changes.append((MOD, os.path.join(prefix, k), self[k].clone(holding_collection), end_collection[k].clone(holding_collection))) + changes.append((MOD, os.path.join(prefix, k), self[k].clone(holding_collection, ""), end_collection[k].clone(holding_collection, ""))) else: - changes.append((ADD, os.path.join(prefix, k), end_collection[k].clone(holding_collection))) + changes.append((ADD, os.path.join(prefix, k), end_collection[k].clone(holding_collection, ""))) return changes @must_be_writable @@ -937,12 +999,14 @@ class RichCollectionBase(CollectionBase): alternate path indicating the conflict. """ + if changes: + self._committed = False for change in changes: event_type = change[0] path = change[1] initial = change[2] local = self.find(path) - conflictpath = "%s~conflict-%s~" % (path, time.strftime("%Y-%m-%d-%H:%M:%S", + conflictpath = "%s~%s~conflict~" % (path, time.strftime("%Y%m%d-%H%M%S", time.gmtime())) if event_type == ADD: if local is None: @@ -980,6 +1044,24 @@ class RichCollectionBase(CollectionBase): stripped = self.portable_manifest_text() return hashlib.md5(stripped).hexdigest() + '+' + str(len(stripped)) + @synchronized + def subscribe(self, callback): + if self._callback is None: + self._callback = callback + else: + raise errors.ArgumentError("A callback is already set on this collection.") + + @synchronized + def unsubscribe(self): + if self._callback is not None: + self._callback = None + + @synchronized + def notify(self, event, collection, name, item): + if self._callback: + self._callback(event, collection, name, item) + self.root_collection().notify(event, collection, name, item) + @synchronized def __eq__(self, other): if other is self: @@ -998,6 +1080,12 @@ class RichCollectionBase(CollectionBase): def __ne__(self, other): return not self.__eq__(other) + @synchronized + def flush(self): + """Flush bufferblocks to Keep.""" + for e in self.values(): + e.flush() + class Collection(RichCollectionBase): """Represents the root of an Arvados Collection. @@ -1080,9 +1168,9 @@ class Collection(RichCollectionBase): self._manifest_locator = None self._manifest_text = None self._api_response = None + self._past_versions = set() self.lock = threading.RLock() - self.callbacks = [] self.events = None if manifest_locator_or_text: @@ -1094,7 +1182,7 @@ class Collection(RichCollectionBase): self._manifest_text = manifest_locator_or_text else: raise errors.ArgumentError( - "Argument to CollectionReader must be a manifest or a collection UUID") + "Argument to CollectionReader is not a manifest or a collection UUID") try: self._populate() @@ -1110,6 +1198,10 @@ class Collection(RichCollectionBase): def writable(self): return True + @synchronized + def known_past_version(self, modified_at_and_portable_data_hash): + return modified_at_and_portable_data_hash in self._past_versions + @synchronized @retry_method def update(self, other=None, num_retries=None): @@ -1119,9 +1211,15 @@ class Collection(RichCollectionBase): if self._manifest_locator is None: raise errors.ArgumentError("`other` is None but collection does not have a manifest_locator uuid") response = self._my_api().collections().get(uuid=self._manifest_locator).execute(num_retries=num_retries) + if self.known_past_version((response.get("modified_at"), response.get("portable_data_hash"))): + # We've merged this record this before. Don't do anything. + return + else: + self._past_versions.add((response.get("modified_at"), response.get("portable_data_hash"))) other = CollectionReader(response["manifest_text"]) baseline = CollectionReader(self._manifest_text) self.apply(baseline.diff(other)) + self._manifest_text = self.manifest_text() @synchronized def _my_api(self): @@ -1145,6 +1243,10 @@ class Collection(RichCollectionBase): self._block_manager = _BlockManager(self._my_keep()) return self._block_manager + def _remember_api_response(self, response): + self._api_response = response + self._past_versions.add((response.get("modified_at"), response.get("portable_data_hash"))) + def _populate_from_api_server(self): # As in KeepClient itself, we must wait until the last # possible moment to instantiate an API client, in order to @@ -1154,9 +1256,9 @@ class Collection(RichCollectionBase): # clause, just like any other Collection lookup # failure. Return an exception, or None if successful. try: - self._api_response = self._my_api().collections().get( + self._remember_api_response(self._my_api().collections().get( uuid=self._manifest_locator).execute( - num_retries=self.num_retries) + num_retries=self.num_retries)) self._manifest_text = self._api_response['manifest_text'] return None except Exception as e: @@ -1215,9 +1317,12 @@ class Collection(RichCollectionBase): def __exit__(self, exc_type, exc_value, traceback): """Support scoped auto-commit in a with: block.""" - if exc_type is not None: + if exc_type is None: if self.writable() and self._has_collection_uuid(): self.save() + self.stop_threads() + + def stop_threads(self): if self._block_manager is not None: self._block_manager.stop_threads() @@ -1236,7 +1341,7 @@ class Collection(RichCollectionBase): return self._manifest_locator @synchronized - def clone(self, new_parent=None, readonly=False, new_config=None): + def clone(self, new_parent=None, new_name=None, readonly=False, new_config=None): if new_config is None: new_config = self._config if readonly: @@ -1300,9 +1405,9 @@ class Collection(RichCollectionBase): Retry count on API calls (if None, use the collection default) """ - if self.modified(): + if not self.committed(): if not self._has_collection_uuid(): - raise AssertionError("Collection manifest_locator must be a collection uuid. Use save_new() for new collections.") + raise AssertionError("Collection manifest_locator is not a collection uuid. Use save_new() for new collections.") self._my_block_manager().commit_all() @@ -1310,13 +1415,13 @@ class Collection(RichCollectionBase): self.update() text = self.manifest_text(strip=False) - self._api_response = self._my_api().collections().update( + self._remember_api_response(self._my_api().collections().update( uuid=self._manifest_locator, body={'manifest_text': text} ).execute( - num_retries=num_retries) + num_retries=num_retries)) self._manifest_text = self._api_response["manifest_text"] - self.set_unmodified() + self.set_committed() return self._manifest_text @@ -1361,36 +1466,24 @@ class Collection(RichCollectionBase): if create_collection_record: if name is None: - name = "Collection created %s" % (time.strftime("%Y-%m-%d %H:%M:%S %Z", time.localtime())) + name = "New collection" + ensure_unique_name = True body = {"manifest_text": text, "name": name} if owner_uuid: body["owner_uuid"] = owner_uuid - self._api_response = self._my_api().collections().create(ensure_unique_name=ensure_unique_name, body=body).execute(num_retries=num_retries) + self._remember_api_response(self._my_api().collections().create(ensure_unique_name=ensure_unique_name, body=body).execute(num_retries=num_retries)) text = self._api_response["manifest_text"] self._manifest_locator = self._api_response["uuid"] self._manifest_text = text - self.set_unmodified() + self.set_committed() return text - @synchronized - def subscribe(self, callback): - self.callbacks.append(callback) - - @synchronized - def unsubscribe(self, callback): - self.callbacks.remove(callback) - - @synchronized - def notify(self, event, collection, name, item): - for c in self.callbacks: - c(event, collection, name, item) - @synchronized def _import_manifest(self, manifest_text): """Import a manifest into a `Collection`. @@ -1420,6 +1513,7 @@ class Collection(RichCollectionBase): segments = [] streamoffset = 0L state = BLOCKS + self.find_or_create(stream_name, COLLECTION) continue if state == BLOCKS: @@ -1445,27 +1539,34 @@ class Collection(RichCollectionBase): raise errors.SyntaxError("File %s conflicts with stream of the same name.", filepath) else: # error! - raise errors.SyntaxError("Invalid manifest format") + raise errors.SyntaxError("Invalid manifest format, expected file segment but did not match format: '%s'" % tok) if sep == "\n": stream_name = None state = STREAM_NAME - self.set_unmodified() + self.set_committed() + + @synchronized + def notify(self, event, collection, name, item): + if self._callback: + self._callback(event, collection, name, item) class Subcollection(RichCollectionBase): """This is a subdirectory within a collection that doesn't have its own API server record. - It falls under the umbrella of the root collection. + Subcollection locking falls under the umbrella lock of its root collection. """ - def __init__(self, parent): + def __init__(self, parent, name): super(Subcollection, self).__init__(parent) self.lock = self.root_collection().lock self._manifest_text = None + self.name = name + self.num_retries = parent.num_retries def root_collection(self): return self.parent.root_collection() @@ -1482,21 +1583,25 @@ class Subcollection(RichCollectionBase): def _my_block_manager(self): return self.root_collection()._my_block_manager() - def notify(self, event, collection, name, item): - return self.root_collection().notify(event, collection, name, item) - def stream_name(self): - for k, v in self.parent.items(): - if v is self: - return os.path.join(self.parent.stream_name(), k) - return '.' + return os.path.join(self.parent.stream_name(), self.name) @synchronized - def clone(self, new_parent): - c = Subcollection(new_parent) + def clone(self, new_parent, new_name): + c = Subcollection(new_parent, new_name) c._clonefrom(self) return c + @must_be_writable + @synchronized + def _reparent(self, newparent, newname): + self._committed = False + self.flush() + self.parent.remove(self.name, recursive=True) + self.parent = newparent + self.name = newname + self.lock = self.parent.root_collection().lock + class CollectionReader(Collection): """A read-only collection object.